I've built a very simple ChIP-seq pipeline using Nextflow, and it generally works. The problem I’m having is ... whenever I attempt to use trim_galore to pre-trim my Input data, I get an error. If I don't include my Input data, I get no error and the pipeline proceeds as it should.
I ran the following:
trim_galore --fastqc $input_file
And the following error is generated:
This is cutadapt 1.9.1 with Python 2.7.11
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Control.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
cutadapt: error: At line 3: Sequence descriptions in the FASTQ file don't match ('ROCKFORD:8:11:11825:13179#0/1' != 'ROCKFORD:8:11:f').
The second sequence description must be either empty or equal to the first description.
gzip: stdout: Broken pipe
Cutadapt terminated with exit signal: '256'.
The other two fastq files are trimmed fine. I'm not entirely sure what to do. I just received these files from the sequencing core so nothing has been done to them. Any thoughts?
1 answer
The error message is fairly clear. Ask the sequencing facility to regenerate the files and then double check that this is fixed before sending it back to you. They should also double check the other files they've produced lately for others.
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I got the same issue after a download on sra:
I have check files with :
Nothing weird ... any idea ?
Either re-fastq-dump the reads with
-Foption to recover original Illumina style fastq headers or get the fastq's from ENA.Yeah this is what I did fastq's from ENA solution and it then worked fine. Thanks